Can molecular modeling go quantum?

(BOSTON) — We tend to regard anything that’s too small to be seen with the naked eye as “microscopic,” but within that realm are all manner of organisms and structures that range in size from individual atoms up to living bacteria. Studying and modeling biology at those different scales is challenging, particularly because the laws of physics that govern the visible world start to break down when considering objects that are the size of only a few atoms. At this scale, the theory of quantum physics is required to make sense of how those tiny objects behave, which has led to the creation of fields like quantum chemistry and modern electronics.

This is a model of ATP synthase, an enzyme that could serve as a model system for incorporating quantum physics into the analysis of biology. Credit: Wyss Institute at Harvard University

Charles Reilly, Ph.D., a molecular biophysicist and visual artist at the Wyss Institute at Harvard University, argues that the notoriously complex world of molecular biology can also be viewed through a quantum perspective, which would allow tools developed for quantum physics to be applied to enhance our understanding of life itself. His essay, “The choreography of life,” is published in the magazine The Biochemist.

“When we look at a single biomolecule, we often disregard the fact that each molecule is made up of many different atoms that are constantly moving around and interacting with each other, and that those specific interactions occur at particular frequencies. These interactions then determine the form and function of the biomolecule as a whole,” says Reilly. “If, instead, we could evaluate the characteristics of the relationships between atoms and the movements of those atoms using quantum mechanical models, we would be able to generate a much more complete picture of what’s going on biologically at the nanoscale and, potentially, across all scales of life.”

Based on collaborative research with the Wyss Institute’s Founding Director, Donald Ingber, M.D., Ph.D., Reilly suggests that all the moving elements in a biological network, like the atoms in a protein molecule, can be thought of not only as structures, but also as springs that contain a certain amount of energy that causes them to extend and retract in a coordinated manner. That oscillation in the spring’s length can be plotted like a wave, giving each atom both a structure-based representation and a wave representation. This “double identity” of physical elements, which mirrors quantum physics’ definition of quanta of light as both particles and waves, can thus potentially allow quantum mechanical tools to be used to understand biological systems.

The Wyss Institute for Biologically Inspired Engineering at Harvard University (http://wyss.harvard.edu) uses Nature’s design principles to develop bioinspired materials and devices that will transform medicine and create a more sustainable world. Wyss researchers are developing innovative new engineering solutions for healthcare, energy, architecture, robotics, and manufacturing that are translated into commercial products and therapies through collaborations with clinical investigators, corporate alliances, and formation of new startups. The Wyss Institute creates transformative technological breakthroughs by engaging in high risk research, and crosses disciplinary and institutional barriers, working as an alliance that includes Harvard’s Schools of Medicine, Engineering, Arts & Sciences and Design, and in partnership with Beth Israel Deaconess Medical Center, Brigham and Women’s Hospital, Boston Children’s Hospital, Dana–Farber Cancer Institute, Massachusetts General Hospital, the University of Massachusetts Medical School, Spaulding Rehabilitation Hospital, Boston University, Tufts University, Charité – Universitätsmedizin Berlin, University of Zurich and Massachusetts Institute of Technology.